DNA barcoding is a technique in which species identification is performed by using DNA sequences from a small fragment of the genome, with the aim of contributing to a wide range of ecological and conservation studies in which traditional taxonomic identification is not practical. DNA barcoding is well established in animals, but there is not yet any universally accepted barcode for plants. Here, we undertook intensive field collections in two biodiversity hotspots (Mesoamerica and southern Africa). Using >1,600 samples, we compared eight potential barcodes. Going beyond previous plant studies, we assessed to what extent a ''DNA barcoding gap'' is present between intra-and interspecific variations, using multiple accessions per species. Given its adequate rate of variation, easy amplification, and alignment, we identified a portion of the plastid matK gene as a universal DNA barcode for flowering plants. Critically, we further demonstrate the applicability of DNA barcoding for biodiversity inventories. In addition, analyzing >1,000 species of Mesoamerican orchids, DNA barcoding with matK alone reveals cryptic species and proves useful in identifying species listed in Convention on International Trade of Endangered Species (CITES) appendixes.

The great majority of plant species in the tropics require animals to achieve pollination, but the exact role of floral signals in attraction of animal pollinators is often debated. Many plants provide a floral reward to attract a guild of pollinators, and it has been proposed that floral signals of non-rewarding species may converge on those of rewarding species to exploit the relationship of the latter with their pollinators. In the orchid family (Orchidaceae), pollination is almost universally animal-mediated, but a third of species provide no floral reward, which suggests that deceptive pollination mechanisms are prevalent. Here, we examine floral colour and shape convergence in Neotropical plant communities, focusing on certain food-deceptive Oncidiinae orchids (e.g. Trichocentrum ascendens and Oncidium nebulosum) and rewarding species of Malpighiaceae. We show that the species from these two distantly related families are often more similar in floral colour and shape than expected by chance and propose that a system of multifarious floral mimicry—a form of Batesian mimicry that involves multiple models and is more complex than a simple one model–one mimic system—operates in these orchids. The same mimetic pollination system has evolved at least 14 times within the species-rich Oncidiinae throughout the Neotropics. These results help explain the extraordinary diversification of Neotropical orchids and highlight the complexity of plant–animal interactions.

Phylogenetic relationships in species complexes and lineages derived from rapid diversifications are often challenging to resolve using morphology or standard DNA barcoding markers. The hyper-diverse genus Lepanthes from Neotropical cloud forest includes over 1200 species and many recent, explosive diversifications that have resulted in poorly supported nodes and morphological convergence across clades. Here, we assess the performance of 446 nuclear-plastid-mitochondrial markers derived from an anchored hybrid enrichment approach (AHE) coupled with coalescence- and species network-based inferences to resolve phylogenetic relationships and improve species recognition in the Lepanthes horrida species group. In addition to using orchid-specific probes to increase enrichment efficiency, we improved gene tree resolution by extending standard angiosperm targets into adjacent exons. We found high topological discordance among individual gene trees, suggesting that hybridization/polyploidy may have promoted speciation in the lineage via formation of new hybrid taxa. In addition, we identified ten loci with the highest phylogenetic informativeness values from these genomes. Most previous phylogenetic sampling in the Pleurothallidinae relies on two regions (ITS and matK), therefore, the evaluation of other markers such as those shown here may be useful in future phylogenetic studies in the orchid family. Coalescent-based species tree estimation methods resolved the phylogenetic relationships of the L. horrida species group. The resolution of the phylogenetic estimations was improved with the inclusion of extended anchor targets. This approach produced longer loci with higher discriminative power. These analyses also disclosed two undescribed species, L. amicitiae and L. genetoapophantica, formally described here, which are also supported by morphology. Our study demonstrates the utility of combined genomic evidence to disentangle phylogenetic relationships at very shallow levels of the tree of life, and in clades showing convergent trait evolution. With a fully resolved phylogeny, is it possible to disentangle traits evolving in parallel or convergently across these orchid lineages such as flower color and size from diagnostic traits such as the shape and orientation of the lobes of the petals and lip.

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The Orchidaceae is one of the most diverse vascular plant families in the Neotropics and the most diverse in Panama. The number of species is triple that of other well-represented families of angiosperms such as Rubiaceae, Fabaceae and Poaceae. Despite its importance in terms of diversity, the latest checklist was published ten years ago and the latest in-depth taxonomic treatments were published in 1949 and 1993. The accumulation of information over the years and the need to update the nomenclature and to clarify taxonomic concepts made necessary the publication of an up-dated checklist of the Orchidaceae of Panama. This checklist was completed by studying specimens strictly collected in Panama and vouchered in herbaria. Species are presented alphabetically with their synonyms and herbarium vouchers. The data were analyzed to explain the patterns of geographic distribution, most diverse taxa, endemism, exotic species and relationships with other nearby floras. The checklist contains 1365 species (including two natural hybrids and three subspecies) in four subfamilies, 16 tribes, 27 subtribes and 187 genera. Four exotic species were recorded. A total of 296 (21.7%) species are endemic. Epidendroideae is the most diverse group housing more than 90% of species. The most diverse subtribes are Pleurothallidinae (30 genera, 405 spp.), Laeliinae (16 genera, 292 spp.), Oncidiinae (29 genera, 157 spp.) and Maxillariinae (18 genera, 132 spp.). The most diverse genera are: Epidendrum (206 spp.), Stelis (88 spp.), Lepanthes (66 spp.) and Pleurothallis (54 spp.). Nomenclatural changes are proposed in Maxillariella, Pleurothallis, Specklinia, Stelis and Trichocentrum. Many areas remain unexplored for orchids, and we estimate that much work remains to complete a floristic treatment that reveals more realistic data on the orchid flora that Panama harbors. This checklist is an important initial step toward the development of an illustrated treatment of the Orchidaceae of Panama.